1. How to define the protein active site How to define the protein active site

The co-crystallized ligand should be used to define the protein active site.

In the case where there is no co-crystallized protein available, it is still possible to predefine an area for the active site. There are two possibilities: the first one is detailed in the user guide and consists to list all the amino acids inside the area; the second is to manually position a probe molecule such as benzene in the center of the area of the active site and to save this molecule as the ligand (mol2 format, to be used in the setup of the protein).

2. Why the layout is wrong with the web platform? Why the layout is wrong?

Even if we try to have a layout that will display correctly on most internet browsers, there are always new versions that we haven't tested or successfully modified our template to support these new versions. Please send us some feedback on your experience with your browser version and OS. You can refer the the user Guide for more details.

3. Score and energy values in FITTED Score and energy values in FITTED

When docking, the energy (using molecular mechanics) and a MatchScore (complementarity of functional groups between ligand and protein) of each proposed orientation/conformation of the ligand is computed and used to select the most likely one. At the end a score (RankScore, see Englebienne P. et al. J. Chem. Inf. Model. 2009, 49, 2564-2571) is computed which is somewhat correlated with the binding energy. Thus, while the energy is used to identify the best pose for the same ligand, the score may used to compare different ligands. As a result, one should consider the pose with the best energy out of the three runs but should use the Score and/or MatchScore to compare different ligands. As the score correlates with binding energy, the lower (more negative), the better. As MatchScore provides information about the complementarity of the ligand and the active site defined as the Interaction Spheres (IS), the higher, the better.

4. Java application not loading in browser Java application not loading in browser

When trying to visualize a molecule with either the 2D Sketcher or the 3D OpenAstex viewer, the Java security needs to be set to Medium in order to allow the execution of the application. 1. Go to the Java Control Panel (On Windows Click Start and then Configure Java). 2. Click on the Security tab. 3. Set to Medium. 4. Apply, Close and restart the browser. If using java version 8 or later, add a site exception (example).